Remove non-standard ext keys and model after quartonotebook

[mahesh-panchal]

PR checklist

Part of #8716

• Removes non-standard ext keys. Inputs should come in through inputs and can override default settings.
• Reports are always parameterized as a result.
• Follows the model of QUARTONOTEBOOK.
• Fixes bug with being able to override the artifacts directory.

---

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the module conventions in the contribution docs
• If necessary, include test data in your PR.
• Remove all TODO statements.
• Broadcast software version numbers to topic: versions - See version_topics
• Follow the naming conventions.
• Follow the parameters requirements.
• Follow the input/output options guidelines.
• Add a resource label
• Use BioConda and BioContainers if possible to fulfil software requirements.
• Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
  • For modules:
    • nf-core modules test <MODULE> --profile docker
    • nf-core modules test <MODULE> --profile singularity
    • nf-core modules test <MODULE> --profile conda
  • For subworkflows:
    • nf-core subworkflows test <SUBWORKFLOW> --profile docker
    • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
    • nf-core subworkflows test <SUBWORKFLOW> --profile conda

[SPPearce]

@mahesh-panchal , I don't really understand what this module is actually doing inside.
Have you checked that the output file is indeed rendered properly?

[mahesh-panchal]

Rendered output:
test_rmd.html

The code is changed so that it's always reading from a params.yml.
By passing a map in through parameters, one can change implicit parameters, and add new ones. It's also coded such that the parameters are written to the script so a user can see in the .sh file what gets written to the params.yml. The rest of the R code is what was already there. Only the indentation has been removed.

[mahesh-panchal]

There was also an issue where the artifacts directory was mutable but it was hard coded, so there was a decision to make - either make artifacts immutable or mutable, and went with mutable, although the code looks cleaner when it's immutable.

[SPPearce]

I think it would be better to just hardcode the artifacts folder.